Contacts of the strand formed by residues 1373 - 1378 (chain E) in PDB entry 6C3P
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS1373 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1371E GLY 2.6 5.5 + - - -
1372E GLN* 1.3 78.4 - - + +
1374E ILE* 1.3 54.9 + - - +
1524E MET* 3.4 42.8 - - + -
1532E VAL* 3.7 8.7 - - + +
1534E THR* 5.4 1.3 - - + -
1544E SER 5.5 0.4 - - - +
1545E ALA* 3.2 6.6 - - + -
1546E ASP* 2.3 43.7 + - - +
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Residues in contact with ILE1374 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1368E ILE* 4.3 24.9 - - + -
1371E GLY* 3.6 19.9 + - - +
1373E LYS* 1.3 78.9 - - - +
1375E GLY* 1.3 63.4 + - - +
1531E THR* 5.8 0.9 - - + -
1532E VAL 3.4 11.1 + - - +
1533E VAL* 3.7 35.4 - - + -
1534E THR* 2.8 26.5 + - - +
1545E ALA* 3.5 4.3 - - - -
1546E ASP* 4.2 4.0 - - + -
1547E LEU* 3.4 38.8 - - + +
1549E ILE* 3.8 23.6 - - + -
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Residues in contact with GLY1375 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1374E ILE* 1.3 70.7 - - - +
1376E ILE* 1.3 58.7 + - - -
1534E THR* 3.2 11.0 - - - -
1542E ILE* 3.5 20.2 - - - -
1545E ALA* 3.5 1.5 - - - +
1547E LEU 2.3 22.5 + - - +
1548E VAL 3.2 1.6 - - - -
1549E ILE* 2.4 37.6 + - - +
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Residues in contact with ILE1376 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1368E ILE* 6.2 0.4 - - + -
1374E ILE* 4.4 0.4 + - + -
1375E GLY* 1.3 74.5 - - - -
1377E CYS* 1.3 69.6 + - - +
1384E LYS* 4.5 1.3 - - + -
1387E PHE* 3.8 32.5 - - + -
1503E ILE* 5.5 0.4 - - + -
1533E VAL* 3.7 26.0 - - + -
1534E THR 2.8 19.9 + - - +
1535E ILE* 3.4 35.5 - - + +
1536E ALA 3.5 3.3 + - - -
1542E ILE* 3.8 2.1 - - - +
1549E ILE* 3.2 47.1 - - + +
1551E LEU* 4.1 21.8 - - + -
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Residues in contact with CYS1377 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1376E ILE* 1.3 78.2 - - - +
1378E GLY* 1.3 62.4 + - - +
1384E LYS* 3.7 15.3 - - - +
1536E ALA 4.1 16.8 - - - +
1539E VAL* 4.8 9.9 - - + -
1542E ILE* 3.7 20.2 - - + -
1548E VAL* 4.2 1.8 - - - -
1549E ILE 2.8 14.4 + - - +
1550E VAL* 4.1 17.7 - - - -
1551E LEU* 3.4 15.6 + - - +
1573E PHE* 3.6 31.9 - - - -
1576E PHE* 5.0 3.1 - - - -
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Residues in contact with GLY1378 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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860E ASP* 4.5 6.1 - - - +
1377E CYS* 1.3 83.1 - - - +
1379E ARG* 1.3 67.6 + - - -
1384E LYS* 3.3 11.5 + - - +
1536E ALA 5.1 3.2 + - - +
1539E VAL* 6.1 0.2 - - - +
1550E VAL* 5.2 0.9 - - - -
1551E LEU 4.1 11.9 - - - -
1576E PHE* 4.3 19.9 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il